AtChem (version 1), an open-source box model for the Master Chemical Mechanism

Roberto Sommariva; Sam Cox; Chris Martin; Kasia Borońska; Jenny Young; Peter K. Jimack; Michael J. Pilling; Vasileios N. Matthaios; Beth S. Nelson; Mike J. Newland; Marios Panagi; William J. Bloss; Paul S. Monks; Andrew R. Rickard

doi:10.5194/gmd-13-169-2020

AtChem (version 1), an open-source box model for the Master Chemical Mechanism

Roberto Sommariva^*, Sam Cox, Chris Martin, Kasia Borońska, Jenny Young, Peter K. Jimack, Michael J. Pilling, Vasileios N. Matthaios, Beth S. Nelson, Mike J. Newland, Marios Panagi, William J. Bloss, Paul S. Monks, Andrew R. Rickard

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

12 Citations (Scopus)

Abstract

AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism (MCM, http://mcm.york.ac.uk/, last access: 16 January 2020). AtChem was initially developed within the EUROCHAMP project as a web application (AtChem-online, https://atchem.leeds.ac.uk/webapp/, last access: 16 January 2020) for modelling environmental chamber experiments; it was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies. AtChem is installed, set up and configured using semi-automated scripts and simple text configuration files, making it easy to use even for inexperienced users. A key feature of AtChem is that it can easily be constrained to observational data which may have different timescales, thus retaining all the information contained in the observations. Implementation of a continuous integration workflow, coupled with a comprehensive suite of tests and version control software, makes the AtChem code base robust, reliable and traceable. The AtChem2 code and documentation are available at https://github.com/AtChem/ (last access: 16 January 2020) under the open-source MIT License.

Original language	English
Pages (from-to)	169-183
Number of pages	15
Journal	Geoscientific Model Development
Volume	13
Issue number	1
DOIs	https://doi.org/10.5194/gmd-13-169-2020
Publication status	Published - 27 Jan 2020

Bibliographical note

Funding Information:
Financial support. Roberto Sommariva, Sam Cox and Paul S. Monks recognise the support of the University of Leicester ReSET programme. Andrew R. Rickard and Mike J. Newland recognise funding from the EU Horizon 2020 research and innovation programme through the EUROCHAMP-2020 Infrastructure Activity (grant agreement no. 730997). Beth S. Nelson recognises the NERC SPHERES Doctoral Training Partnership (DTP) for her studentship.

Publisher Copyright:
© 2020 Author(s).

Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.

ASJC Scopus subject areas

Modelling and Simulation
Earth and Planetary Sciences(all)

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10.5194/gmd-13-169-2020

Cite this

Sommariva, R., Cox, S., Martin, C., Borońska, K., Young, J., Jimack, P. K., Pilling, M. J., Matthaios, V. N., Nelson, B. S., Newland, M. J., Panagi, M., Bloss, W. J., Monks, P. S., & Rickard, A. R. (2020). AtChem (version 1), an open-source box model for the Master Chemical Mechanism. Geoscientific Model Development, 13(1), 169-183. https://doi.org/10.5194/gmd-13-169-2020

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title = "AtChem (version 1), an open-source box model for the Master Chemical Mechanism",

abstract = "AtChem is an open-source zero-dimensional box model for atmospheric chemistry. Any general set of chemical reactions can be used with AtChem, but the model was designed specifically for use with the Master Chemical Mechanism (MCM, http://mcm.york.ac.uk/, last access: 16 January 2020). AtChem was initially developed within the EUROCHAMP project as a web application (AtChem-online, https://atchem.leeds.ac.uk/webapp/, last access: 16 January 2020) for modelling environmental chamber experiments; it was recently upgraded and further developed into a stand-alone offline version (AtChem2), which allows the user to run complex and long simulations, such as those needed for modelling of intensive field campaigns, as well as to perform batch model runs for sensitivity studies. AtChem is installed, set up and configured using semi-automated scripts and simple text configuration files, making it easy to use even for inexperienced users. A key feature of AtChem is that it can easily be constrained to observational data which may have different timescales, thus retaining all the information contained in the observations. Implementation of a continuous integration workflow, coupled with a comprehensive suite of tests and version control software, makes the AtChem code base robust, reliable and traceable. The AtChem2 code and documentation are available at https://github.com/AtChem/ (last access: 16 January 2020) under the open-source MIT License.",

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note = "Funding Information: Financial support. Roberto Sommariva, Sam Cox and Paul S. Monks recognise the support of the University of Leicester ReSET programme. Andrew R. Rickard and Mike J. Newland recognise funding from the EU Horizon 2020 research and innovation programme through the EUROCHAMP-2020 Infrastructure Activity (grant agreement no. 730997). Beth S. Nelson recognises the NERC SPHERES Doctoral Training Partnership (DTP) for her studentship. Publisher Copyright: {\textcopyright} 2020 Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",

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AU - Pilling, Michael J.

AU - Matthaios, Vasileios N.

AU - Nelson, Beth S.

AU - Newland, Mike J.

AU - Panagi, Marios

AU - Bloss, William J.

AU - Monks, Paul S.

AU - Rickard, Andrew R.

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AtChem (version 1), an open-source box model for the Master Chemical Mechanism

Abstract

Bibliographical note

ASJC Scopus subject areas

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